7R3A

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Methanococcus maripaludis in complex with inosine

PDB DOI: https://doi.org/10.2210/pdb7R3A/pdb

Classification: HYDROLASE
Organism(s): Methanococcus maripaludis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-06 Released: 2023-02-15
Deposition Author(s): Saleem-Batcha, R., Popadic, D., Andexer, J.N.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.243
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with inosine

Saleem-Batcha, R., Popadic, D., Andexer, J.N.

To be published.

Macromolecule Content

Total Structure Weight: 393.5 kDa
Atom Count: 26,142
Modelled Residue Count: 3,288
Deposited Residue Count: 3,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-inosyl-L-homocysteine hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	435	Methanococcus maripaludis	Mutation(s): 0 Gene Names: ahcY, MMP0920 EC: 3.13.1.9
UniProt
Find proteins for Q6LYR8 (Methanococcus maripaludis (strain S2 / LL)) Explore Q6LYR8 Go to UniProtKB: Q6LYR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6LYR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	CA [auth G] FA [auth H] J [auth A] M [auth B] P [auth C] CA [auth G], FA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], W [auth E], Z [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]
NOS (Subject of Investigation/LOI) Query on NOS Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F]	BA [auth G] EA [auth H] I [auth A] L [auth B] O [auth C] BA [auth G], EA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], V [auth E], Y [auth F]	INOSINE C₁₀ H₁₂ N₄ O₅ UGQMRVRMYYASKQ-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Y [auth F]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	AA [auth G] DA [auth H] K [auth A] N [auth B] Q [auth C] AA [auth G], DA [auth H], K [auth A], N [auth B], Q [auth C], T [auth D], U [auth E], X [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain X [auth F]